Contacts of the strand formed by residues 159 - 162 (chain P) in PDB entry 5A0Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 159 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36P GLY 3.6 9.4 - - - +
37P ILE* 4.3 9.2 - - + +
145P LEU* 3.7 1.3 - - - -
157P TRP* 2.2 40.9 - - - -
158P LYS* 1.3 80.8 - - + +
160P THR* 1.4 55.2 - - - +
173P LEU* 4.0 27.8 - - + +
177P TYR* 4.4 6.3 - - + -
55Q LEU* 3.7 20.3 + - + +
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Residues in contact with THR 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P GLY 3.0 28.8 + - - +
134P LEU* 3.4 32.1 - - + -
145P LEU* 3.8 22.2 - - + -
146P PHE 5.1 0.9 - - - +
147P GLN* 4.0 7.3 + - - -
157P TRP* 3.5 36.7 + - + -
159P ALA* 1.4 75.8 - - - +
161P ALA* 1.4 66.0 + - - +
170P LYS* 3.6 11.2 + - - -
173P LEU* 3.3 13.2 - - - +
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Residues in contact with ALA 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P SER 3.6 12.6 - - - +
35P VAL* 4.2 6.1 - - + +
134P LEU* 5.1 0.2 - - - -
160P THR* 1.4 77.4 + - - +
162P MET* 1.3 69.9 + - - +
166P TYR* 3.6 16.0 - - + +
169P GLY* 4.1 6.5 - - - -
170P LYS* 3.2 45.6 + - + +
173P LEU* 4.0 10.5 - - + -
193P THR* 5.3 0.2 - - + -
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Residues in contact with MET 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P VAL* 5.4 3.4 - - + -
33P PRO* 3.1 4.3 - - - +
34P SER* 2.3 53.9 + - - +
74P VAL 3.5 11.7 - - - +
76P SER* 3.4 13.0 - - - +
132P SER* 3.6 10.3 - - - +
133P LEU* 3.6 7.9 - - - -
134P LEU* 2.9 42.4 - - + +
147P GLN* 2.6 50.0 - - - +
161P ALA* 1.3 77.3 - - - +
163P GLY* 1.3 60.0 + - - +
164P LYS 4.4 0.7 - - - +
166P TYR* 3.9 8.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il